"The air traffic control centre directs the planes when they leave the airport and are up in the air. When we reach a critical point, we must limit the number of aircraft for safety reasons. It usually happens when we are short four to five people," said Per Fröberg, press officer at the Swedish Civil Aviation Administration (Luftfartsverket, LFV).
The reason for the staff shortage is the lack of cover for sick staff, according to Fröberg.
All flights, including domestic, foreign and overflight traffic, will be hit by delays until at least 3pm.
"There are four morning departures to Umeå, Malmö, Luleå and Gothenburg. They have been cancelled in both directions. We are doing our best now to book all customers onto later flights," said Anders Lindström, press spokesman for the airline.
Travellers are advised to go to the airport or visit airline websites for more information.
Air traffic at Arlanda has encountered several delays since last month due to a shortage of staff at the air control center in Stockholm, according to Peter Lennartsson, president of the Swedish Union of Civil Servants' (Statstjänstemannaförbundet - ST) flight management arm.
"We have had a large shortage of staff for several years. They have worked on recruiting, but have never successfully had a full team. At the end of the year, there will be a shortage of 10 to 12 people," he said.
The supply of controllers is less than the demand, added Lennartsson. More controllers are currently being trained, but it will take some time before they can start working.
"Our job is flight safety and when there are too few people, we have to cut down on the number of flights," said Lennartsson.